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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 18:24:06 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.60     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 15
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R15_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R15_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R15_1-60A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:    15
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.6000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R15_1-70A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.054 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.194 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.839 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.212 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.390 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.388 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.048 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                           15
Number of "free" reflections       1404
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.909 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.31155288    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                41.1
Norm of Geom. positional gradient                79.1
Norm of X_ray B-factor gradient                  125.
Norm of Geom. B-factor gradient                 0.221E+05
Product of X_ray and Geom posit. gradients     -0.137E+08
 Cosine of angle between them                      -0.435
Product of X_ray and Geom B-fact gradients     -0.421E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8730E+06 GEOM=     0.2636E+05 TOTAL=     0.8993E+06
 function value    899335.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.765     1.644
Bond angles  : others                          3242     2.339     1.582
Torsion angles, period  1. refined              184     6.960     5.000
Torsion angles, period  2. refined               90    35.969    22.778
Torsion angles, period  3. refined              268    13.678    15.000
Torsion angles, period  4. refined                9    11.888    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   303     0.267     0.200
VDW repulsions.others                          1339     0.230     0.200
VDW; torsion: refined_atoms                     730     0.171     0.200
VDW; torsion.others                             707     0.082     0.200
HBOND: refined_atoms                            225     0.194     0.200
HBOND.others                                      1     0.078     0.200
VDW repulsions: symmetry: refined_atoms           7     0.243     0.200
VDW repulsions: symmetry: others                 22     0.195     0.200
HBOND: symmetry: refined_atoms                   25     0.198     0.200
M. chain bond B values: refined atoms           745     1.639     1.387
M. chain bond B values: others                  745     1.637     1.387
M. chain angle B values: refined atoms          926     2.610     2.065
M. chain angle B values: others                 927     2.609     2.065
S. chain bond B values: refined atoms           811     2.893     1.775
S. chain bond B values: others                  810     2.886     1.774
S. chain angle B values: refined atoms         1177     4.512     2.499
S. chain angle B values: others                1178     4.510     2.499
Long range B values: refined atoms             1858     7.320    19.736
Long range B values: others                    1766     6.920    18.297
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    1.2657
Partial structure    1: scale =     0.3890, B  =   47.7152
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3607 100.00   431.2   439.8  0.17  0.17     175   476.4   485.3  0.19  0.21
 0.147    6109  99.97   258.9   243.3  0.17  0.15     335   265.7   250.1  0.21  0.18
 0.244    7777 100.00   167.9   151.8  0.19  0.17     441   163.0   150.6  0.21  0.19
 0.342    9137 100.00    71.6    86.0  0.33  0.26     453    70.3    84.9  0.37  0.29
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2629   0.903    978   0.797   3607   0.874  0.944  0.9674  0.9672  0.9208  0.9353
  0.1468   5123   0.881    986   0.790   6109   0.866  1.024  0.9514  0.9611  0.9056  0.9392
  0.2444   6782   0.874    995   0.769   7777   0.861  1.057  0.9455  0.9576  0.9020  0.9378
  0.3419   8162   0.676    980   0.597   9142   0.667  0.705  0.8519  0.8694  0.8037  0.8536
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26634
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0075
Overall R factor                     =     0.1943
Free R factor                        =     0.2214
Average Fourier shell correlation    =     0.9294
AverageFree Fourier shell correlation=     0.9194
Overall weighted R factor            =     0.1680
Free weighted R factor               =     0.1955
Overall weighted R2 factor           =     0.1972
Free weighted R2 factor              =     0.2314
Average correlation coefficient      =     0.9089
Overall correlation coefficient      =     0.9574
Free correlation coefficient         =     0.9462
Cruickshanks DPI for coordinate error=     0.0976
DPI based on free R factor           =     0.0946
Overall figure of merit              =     0.7975
ML based su of positional parameters =     0.0700
ML based su of thermal parameters    =     2.1014
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134311.56       26356.689       899335.13      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.38594788    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    875411.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0319
Partial structure    1: scale =     0.3888, B  =   47.4988
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1939
Free R factor                        =     0.2205
Average Fourier shell correlation    =     0.9419
AverageFree Fourier shell correlation=     0.9316
Average correlation coefficient      =     0.9103
Overall figure of merit              =     0.8337
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133166.75       9874.2793       875411.81       899335.13    


     CGMAT cycle number =      3

 Weight matrix   0.39977112    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872885.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0186
Partial structure    1: scale =     0.3893, B  =   43.2613
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1927
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9444
AverageFree Fourier shell correlation=     0.9338
Average correlation coefficient      =     0.9127
Overall figure of merit              =     0.8405
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132854.56       9377.2354       872885.75       875411.81    


     CGMAT cycle number =      4

 Weight matrix   0.36693579    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    793730.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0000
Partial structure    1: scale =     0.3893, B  =   43.2598
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1923
Free R factor                        =     0.2195
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9344
Average correlation coefficient      =     0.9137
Overall figure of merit              =     0.8421
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132758.92       9287.6396       793730.19       872885.75    


     CGMAT cycle number =      5

 Weight matrix   0.33382803    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722281.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0017
Partial structure    1: scale =     0.3898, B  =   43.1305
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1926
Free R factor                        =     0.2196
Average Fourier shell correlation    =     0.9451
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9137
Overall figure of merit              =     0.8423
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132778.11       9048.3799       722281.06       793730.19    


     CGMAT cycle number =      6

 Weight matrix   0.33452651    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722206.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0000
Partial structure    1: scale =     0.3898, B  =   43.1308
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1930
Free R factor                        =     0.2196
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9346
Average correlation coefficient      =     0.9134
Overall figure of merit              =     0.8425
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    132821.03       8743.0117       722206.25       722281.06    


     CGMAT cycle number =      7

 Weight matrix   0.33458617    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722251.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0003
Partial structure    1: scale =     0.3895, B  =   43.1652
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1931
Free R factor                        =     0.2195
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9347
Average correlation coefficient      =     0.9134
Overall figure of merit              =     0.8425
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    132843.48       8670.1533       722211.94       722206.25    
 fvalues    132843.48       8670.1533       722211.94       722254.00    


     CGMAT cycle number =      8

 Weight matrix   0.33559966    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722206.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0064
Partial structure    1: scale =     0.3895, B  =   43.1519
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1932
Free R factor                        =     0.2195
Average Fourier shell correlation    =     0.9451
AverageFree Fourier shell correlation=     0.9349
Average correlation coefficient      =     0.9134
Overall figure of merit              =     0.8428
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    132840.98       8635.6553       722206.06       722254.00    


     CGMAT cycle number =      9

 Weight matrix   0.33577543    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722198.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0079
Partial structure    1: scale =     0.3894, B  =   43.1156
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1933
Free R factor                        =     0.2195
Average Fourier shell correlation    =     0.9452
AverageFree Fourier shell correlation=     0.9349
Average correlation coefficient      =     0.9134
Overall figure of merit              =     0.8429
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    132842.84       8617.6475       722198.06       722206.06    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.912 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.33587852    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                39.0
Norm of Geom. positional gradient                39.0
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  110.
Product of X_ray and Geom posit. gradients     -0.148E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.393E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7136E+06 GEOM=      8611.     TOTAL=     0.7222E+06
 function value    722180.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.777     1.644
Bond angles  : others                          3242     1.504     1.582
Torsion angles, period  1. refined              184     6.935     5.000
Torsion angles, period  2. refined               90    35.526    22.778
Torsion angles, period  3. refined              268    13.065    15.000
Torsion angles, period  4. refined                9    12.048    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.267     0.200
VDW repulsions.others                          1364     0.203     0.200
VDW; torsion: refined_atoms                     730     0.172     0.200
VDW; torsion.others                             793     0.083     0.200
HBOND: refined_atoms                            230     0.192     0.200
HBOND.others                                      1     0.130     0.200
VDW repulsions: symmetry: refined_atoms           7     0.241     0.200
VDW repulsions: symmetry: others                 20     0.203     0.200
HBOND: symmetry: refined_atoms                   26     0.196     0.200
M. chain bond B values: refined atoms           745     1.701     1.507
M. chain bond B values: others                  745     1.698     1.507
M. chain angle B values: refined atoms          926     2.690     2.248
M. chain angle B values: others                 927     2.688     2.248
S. chain bond B values: refined atoms           811     2.997     1.897
S. chain bond B values: others                  810     2.991     1.896
S. chain angle B values: refined atoms         1177     4.622     2.682
S. chain angle B values: others                1178     4.620     2.681
Long range B values: refined atoms             1867     7.396    21.310
Long range B values: others                    1770     6.977    19.770
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0090
Partial structure    1: scale =     0.3892, B  =   43.0253
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3607 100.00   431.5   440.2  0.17  0.18     175   476.7   485.2  0.19  0.20
 0.147    6109  99.97   259.1   243.5  0.17  0.15     335   265.9   250.1  0.20  0.18
 0.244    7777 100.00   168.0   151.9  0.19  0.17     441   163.0   150.1  0.21  0.18
 0.342    9137 100.00    71.6    85.8  0.32  0.26     453    70.3    85.1  0.36  0.29
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2629   0.923    978   0.829   3607   0.897  0.947  0.9715  0.9716  0.9214  0.9347
  0.1468   5123   0.885    986   0.795   6109   0.871  1.024  0.9528  0.9622  0.9077  0.9399
  0.2444   6782   0.886    995   0.784   7777   0.873  1.057  0.9500  0.9607  0.9052  0.9371
  0.3419   8162   0.786    980   0.705   9142   0.777  0.754  0.8929  0.9102  0.8150  0.8673
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26634
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0075
Overall R factor                     =     0.1933
Free R factor                        =     0.2194
Average Fourier shell correlation    =     0.9452
AverageFree Fourier shell correlation=     0.9349
Overall weighted R factor            =     0.1681
Free weighted R factor               =     0.1942
Overall weighted R2 factor           =     0.1978
Free weighted R2 factor              =     0.2312
Average correlation coefficient      =     0.9135
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9471
Cruickshanks DPI for coordinate error=     0.0971
DPI based on free R factor           =     0.0937
Overall figure of merit              =     0.8429
ML based su of positional parameters =     0.0612
ML based su of thermal parameters    =     1.7935
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    132840.73       8611.0293       722180.06       722198.06    

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.912 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R15_1-60A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.777     1.644
Bond angles  : others                          3242     1.504     1.582
Torsion angles, period  1. refined              184     6.936     5.000
Torsion angles, period  2. refined               90    35.499    22.778
Torsion angles, period  3. refined              268    13.030    15.000
Torsion angles, period  4. refined                9    12.058    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.267     0.200
VDW repulsions.others                          1364     0.203     0.200
VDW; torsion: refined_atoms                     731     0.172     0.200
VDW; torsion.others                             797     0.083     0.200
HBOND: refined_atoms                            230     0.191     0.200
HBOND.others                                      1     0.132     0.200
VDW repulsions: symmetry: refined_atoms           7     0.241     0.200
VDW repulsions: symmetry: others                 20     0.204     0.200
HBOND: symmetry: refined_atoms                   26     0.198     0.200
M. chain bond B values: refined atoms           745     1.701     1.507
M. chain bond B values: others                  745     1.697     1.507
M. chain angle B values: refined atoms          926     2.688     2.248
M. chain angle B values: others                 927     2.687     2.248
S. chain bond B values: refined atoms           811     2.996     1.896
S. chain bond B values: others                  810     2.990     1.896
S. chain angle B values: refined atoms         1177     4.620     2.681
S. chain angle B values: others                1178     4.618     2.681
Long range B values: refined atoms             1868     7.393    21.313
Long range B values: others                    1771     6.972    19.775
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0109
Partial structure    1: scale =     0.3893, B  =   42.9874
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3607 100.00   431.5   440.2  0.17  0.18     175   476.6   485.2  0.19  0.20
 0.147    6109  99.97   259.1   243.5  0.17  0.15     335   265.9   250.1  0.20  0.18
 0.244    7777 100.00   168.0   151.9  0.19  0.17     441   163.0   150.1  0.21  0.18
 0.342    9137 100.00    71.6    85.7  0.32  0.26     453    70.3    85.1  0.36  0.29
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2629   0.923    978   0.830   3607   0.897  0.947  0.9716  0.9716  0.9216  0.9347
  0.1468   5123   0.885    986   0.795   6109   0.871  1.024  0.9528  0.9622  0.9076  0.9398
  0.2444   6782   0.886    995   0.784   7777   0.873  1.057  0.9500  0.9607  0.9052  0.9370
  0.3419   8162   0.786    980   0.705   9142   0.777  0.754  0.8930  0.9102  0.8151  0.8675
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26634
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0075
Overall R factor                     =     0.1933
Free R factor                        =     0.2193
Average Fourier shell correlation    =     0.9452
AverageFree Fourier shell correlation=     0.9350
Overall weighted R factor            =     0.1681
Free weighted R factor               =     0.1941
Overall weighted R2 factor           =     0.1978
Free weighted R2 factor              =     0.2311
Average correlation coefficient      =     0.9135
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9471
Cruickshanks DPI for coordinate error=     0.0971
DPI based on free R factor           =     0.0937
Overall figure of merit              =     0.8430
ML based su of positional parameters =     0.0612
ML based su of thermal parameters    =     1.7935
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.90
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1943   0.2214   0.797      134312.    7247.9   0.0122  0.916   1.765  1.029   0.087
       1   0.1939   0.2205   0.834      133167.    7210.4   0.0124  0.929   1.760  1.027   0.088
       2   0.1927   0.2198   0.840      132855.    7200.6   0.0134  1.002   1.810  1.058   0.091
       3   0.1923   0.2195   0.842      132759.    7197.6   0.0135  1.017   1.834  1.072   0.092
       4   0.1926   0.2196   0.842      132778.    7196.6   0.0130  0.978   1.819  1.063   0.090
       5   0.1930   0.2196   0.842      132821.    7195.4   0.0124  0.934   1.789  1.044   0.088
       6   0.1931   0.2195   0.843      132843.    7195.5   0.0124  0.930   1.781  1.040   0.088
       7   0.1932   0.2195   0.843      132841.    7193.9   0.0124  0.928   1.778  1.038   0.088
       8   0.1933   0.2195   0.843      132843.    7193.6   0.0124  0.928   1.777  1.038   0.088
       9   0.1933   0.2194   0.843      132841.    7193.2   0.0124  0.928   1.777  1.038   0.088
      10   0.1933   0.2193   0.843      132839.    7192.8   0.0124  0.928   1.777  1.038   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1943   0.1933
             R free    0.2214   0.2193
     Rms BondLength    0.0122   0.0124
      Rms BondAngle    1.7654   1.7765
     Rms ChirVolume    0.0873   0.0878
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      50.3s System:    0.1s Elapsed:     0:51